Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.08 kDa 
• Atom Count: 4920 
• Modelled Residue Count: 592 
• Deposited Residue Count: 620 
• Unique protein chains: 1

1S4C

YHCH PROTEIN (HI0227) COPPER COMPLEX

• PDB DOI: 10.2210/pdb1S4C/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-15 Released: 2005-06-14 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Toedt, J., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 

Literature

Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism.

Teplyakov, A., Obmolova, G., Toedt, J., Galperin, M.Y., Gilliland, G.L.

(2005) J Bacteriol 187: 5520-5527

• PubMed: 16077096 
• DOI: 10.1128/JB.187.16.5520-5527.2005
• Primary Citation of Related Structures:  
  1JOP, 1S4C


• PubMed Abstract: 
  

The yhcH gene is part of the nan operon in bacteria that encodes proteins involved in sialic acid catabolism. Determination of the crystal structure of YhcH from Haemophilus influenzae was undertaken as part of a structural genomics effort in order to assist with the functional assignment of the protein. The structure was determined at 2.2-A resolution by multiple-wavelength anomalous diffraction. The protein fold is a variation of the double-stranded beta-helix. Two antiparallel beta-sheets form a funnel opened at one side, where a putative active site contains a copper ion coordinated to the side chains of two histidine and two carboxylic acid residues. A comparison to other proteins with a similar fold and analysis of the genomic context suggested that YhcH may be a sugar isomerase involved in processing of exogenous sialic acid.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and National Institute of Standards and Technology, Rockville, Maryland, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein HI0227	A, B, C, D	155	Haemophilus influenzae	Mutation(s): 0  Gene Names: HI0227
UniProt
Find proteins for P44583 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44583  Go to UniProtKB:  P44583

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	E [auth A], G [auth B], H [auth C], I [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.9	α = 90
b = 153.9	β = 112.9
c = 53.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-15 
• Released Date: 2005-06-14 
Deposition Author(s): Teplyakov, A., Obmolova, G., Toedt, J., Gilliland, G.L.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance